Add log fold-change calculation to SMaSH

code/run-smash.R

@@ -78,6 +78,7 @@ run_smash <- function(sce, pars) {
                        restrict_top = tuple("local", as.integer(20)))
   })
 
+
   raw_cluster_mgs <- out[[2]]
 
   cluster_mgs <- tibble::as_tibble(raw_cluster_mgs)
@@ -91,9 +92,11 @@ run_smash <- function(sce, pars) {
 
   result <- dplyr::arrange(result, cluster)
 
+  lfcs <- calculate_log_fc(sce, genes = result$gene, clusters = result$cluster)
+
   result <- dplyr::mutate(
     result,
-    log_fc = 0,
+    log_fc = lfcs,
     raw_statistic = 0,
     scaled_statistic = 0,
     p_value = 0,